What you're suggesting isn't impossible, just wildly difficult. It would involve branching the campaign with the only changes in each branch being the number of captured ships available. Of course, if you wanted a ten mission campaign with each possible course mapped out you could have anywhere from a hundred to several thousand slightly varied missions, but I guess it's up to you.
If you want my opinion though, do what karajorma suggested, and just say that the captured fighters are reverse engineered or something, or limit the number of captures you can make to one, and limit the potyential availablility of the fighter to a single one (for Alpha 1).